<ds:KeyInfo>
    <wsse:SecurityTokenReference>
        <wsse:Reference URI="#b3f74c53-b79f-4dec-aa26-ca552f8f8745"/>
    </wsse:SecurityTokenReference>
</ds:KeyInfo>
<ds:Object Id="id1"> // <-Remove this
    <wsu:Timestamp>
        <wsu:Created>2017-03-28T20:21:44Z</wsu:Created>
         <wsu:Expires>2017-03-28T23:08:24Z</wsu:Expires>
        </wsu:Timestamp>
 </ds:Object>  // <-Remove this

Node node = xml.getElementById("id1");
xml.getDocumentElement().removeChild(node);

Org.w3c.dom.DOMException: NOT_FOUND_ERR: An attempt is made to reference a node in a context where it does not exist.